[Chimera-users] Minimize with fixed atoms

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Apr 2 18:30:46 PDT 2012

Hi there,

I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to <5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms.

Am I in a local minima? Is that why nothing moves?

The energy is very high (from the Reply Log):

Potential energy: 222274199.525130, Gradient norm: 833984762.552943
Updated 6029 atoms.  RMSD: 0.000000
Finished 1 of 5 steepest descent minimization steps

Any ideas? I do have some hetero atoms...


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

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